


And along came the spiders

by spiderwriters



Category: Iron Man (Movies), Marvel Cinematic Universe, Spider-Man: Homecoming (2017), The Avengers (Marvel Movies)
Genre: Angst, Gender Dysphoria, Gender Identity, Gender Issues, Hydra (Marvel), Identity Issues, Parent Tony, Parent Tony Stark, Peter Needs a Hug, Post-Spider-Man: Homecoming, Protective Tony Stark, Tony Stark Has A Heart
Language: English
Status: In-Progress
Published: 2018-03-22
Updated: 2018-03-31
Packaged: 2019-04-06 14:00:05
Rating: Teen And Up Audiences
Warnings: No Archive Warnings Apply
Chapters: 2
Words: 3,429
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/14058501
Author URL: https://archiveofourown.org/users/spiderwriters/pseuds/spiderwriters
Summary: Things were looking up for Peter until he woke up in an unfamilar location. It all went down hill when he realized that he had woken up in a Hydra facility. Much to his horror he discovers that he not only is one of many clones of Peter that reratains all of Peter's memories, but is actually a female clone. With this realization and a massive escape with the other clones, there are a lot of broken pieces to pick up.





	1. Chapter 1

**Author's Note:**

> There are multiple chapters coming I'm just new to the site and don't know how to do chapter 1/? yet.

To Peter, everything felt like a an endless floating abyss. He couldn't feel anything, in fact he could hardly think. It was like his mind was running through the thickest sludge in the world. He tried opening his eyes, but any connection to his body lost in this void was futile. Peter's mind tried reaching out to his body, for a connection, any sort of connection. Nothing.

A thought rushed through his consciousness. He wasn't dead, was he? It would explain a few- no, he couldn't be dead. Well, then what had happened? What would cause this to happen?

Peter tried scanning back through his memories. He remembered putting on his Iron Man hand blasters and attending the Stark Expo. He remembered the excitement of standing in the crowd looking at the Iron Man suits made to represent the branches of the military. He remembered the chaos of the night, him facing down a rogue suit, blaster ready. Mr. Stark's voice range clear as the day he heard it. "Good job kid."

Peter felt a tingle sensation run through him. For an instant, he felt a connection. Maybe he wasn't dead after all. Maybe this was helping. He needed to keep this up.

The bright blue hole in the sky was as clear to him as the day it had happened. He remembered being pulled down the stairs quickly by his aunt and uncle, his preteen legs barely being able to keep up. There was an Iron Man action figure still clutched in his hand as they took shelter down in the nearest subway station. As concrete dust and debris rained down on them. His hand clutched the action figure in his hands. He could still remember the warmth of the embrace of his aunt and uncle. It felt like ages before what they eventually called "The Battle of New York" would be over, leaving the city streets in ruin near Stark Tower. At least school had been canceled for a few days seeing as the streets were still filled with alien debris.

There it was again. This time, the tingling stuck around in his fingertips. There was progress after all. What a relief.

Peter remembered that fateful field trip that had almost gone perfectly for once. He was waiting in line to get back on the bus when he notice a red and blue spider crawl from his hoodie onto his hand. Before he could even react, he felt pain run down his arm. He remembered the agony and the flu like symptoms he had experienced. Aunt May was in a fuss when she saw the rash and rushed him to the doctor. Uncle Ben had gotten him his favorite candy bar from the vending machine as they waited to go back. Of course his aunt was trying everything in her power to make sure he got seen as soon as possible. Peter remembered glancing up at the television. There was a news broadcast . Live video of a town floating into the air could be seen. He recognized the flying suits of Iron Man and War Machine in an instant. Before he could find out more on what was eventually called the Sacovia incident, he was brought back to the doctor.

By now there was more to him. He could feel part of his hands, his feet, even some of his core. It radiated and pulsed.

His memories were flashing by now, like someone had pushed fast forward on a video. Coming home and meeting Iron Man face to face, flying to Germany, fighting at the airport. Peter remembering him and Ned trying to figure out if Liz had gotten a new shirt and getting caught by MJ. He recalled the fear of having the Vulture carry him up to the air and having him plummet into the pond. He remembered Liz drilling him on echolocation questions on the bus trip to DC. Peter remembered the grate shame and disappointment in himself seeing how badly he had let Mr. Stark down after the weapon bust went so far south. There was the suffocating panic and fear when the warehouse collapsed on him. He remembered staying up late drinking one to many energy drinks and studying for his chem test on the ceiling last week. Most importantly, he remembered fighting some thugs at trying to steal some armored car. Peter remembered getting cut by one of the thug's weapons. Had it had something on it?

After what felt like ages in the abyss, the sense of, well body sense was starting to return. He could feel his body. It felt like a miracle when he felt his heart beat in his chest, the sound of his breath in his ears, his hair tickling his face. He was still shrouded in darkness though. He could feel that his eyelids we're closed. He forced them to open.

Bright light nearly blinded the poor boy as his eyelids cracked open. Curse his super sensitivity. Maybe he was back at the complex. Just by the smell and the sense of cold around him, he could tell this was a sterile environment. These had to be the bright lights of a hospital room. But where was he exactly?

Peter's sense of sound came back in a rush. It was like he was underwater, only hearing the sounds of his body, and then suddenly thrust to the surface. He could hear the humming of what he assumed to be medical machines, the buzzing of the lights above, water running through the pipes in the walls nearby.

Things finally had sunk into place. He was on some sort of bed that was at an upward incline. Peter wasn't necessarily standing, but not entirely laying down. It was some strange limbo state. He could feel the tight fabric of his costume against his skin, even catching a glimpse of its red color from the corner of his eye. As his eyes adjusted he noticed someone in front of him.

Was it Mr. Stark? No, it couldn't be. The body shape was all wrong. He was shorter, more portly, nothing like the tall and defined figure of Mr. Stark. It could be Happy. But when his eyes focused on the person, Peter realized, it wasn't someone he knew at all. He had wisps of light brown hair, small round spectacles pressed up against his nose. The man wore a suit that seemed slightly out of fashion. It was like he had stepped out from some other place in time. Who was this guy? Peter's eyes must have been playing tricks on him because he swore he saw the man flicker for a moment.

"Ah, ze subject is awake." the man said with a thick German accent. "Good good. Now my dear, how are you feeling?"

How odd? Maybe he was still out of it but it felt weird hearing someone call him dear, especially another guy. Maybe it was a German thing. Everything was sill so... floaty maybe he was making this more weird than it actually was.

The man was quiet for a moment and he spoke to himself. "Note, the subject Drew remains in a state of disorientation after waking. This is roughly thirty -three minutes and twenty two seconds since serum 27x38z2 was administered. Subject Drew's metabolism appears to mimic the calculated results as arousal time is one third of the time for standard non enhanced subjects. Further tests will need to be preformed."

Subject Drew? Peter didn't like the sound of that. Not one bit. There was no way he was going to be called that at the complex, not unless they were trying to keep his identity a secret. But why not call him Spider-Man then?

"Drew?" was all Peter could manage to say.

His voice sounded unnatural. It cracked, and sounded rough and higher than normal. Maybe it was the meds he was on.

The man stepped closer to him. There was a small light shown in Peter's eyes and the man held a finger in front of his face.

"Follow my finger please." the thick German accent said.

Peter forced himself to follow the movement of the finger. As the exercise went on, the speed would vary from a slow crawl to rapid directional changes. Fortunately though, he had regained enough motor function to preform it quite well, at least he thought.

"Where's Mr. Stark?" Peter asked.

His voice still sounded off. It was less scratchy at this point, but still sounded off. At least it was progress. That's all this day seemed to be was slow, monotonous progress.

The man had a look of surprise on his face. His eyes were calculating unknown thoughts behind his round spectacles.

"He is not here at ze moment. Now, tell me, vat all do you remember? Let us start with a name." The man asked.

"It's-" Peter hesitated.

He didn't even know where he was at. For all he knew he had been kidnapped by the thugs from earlier. Maybe this was all a trick to get him to reveal his secret identity. Why should he trust this guy?

It was as though the man could sense his thoughts.

"Ah, I understand. Trust is a hard thing to earn in an unfamiliar place. Just tell me, do you know your name?" the man asked.

Peter nodded. His hair tickled the back of his neck further down than he expected. Huh, he was really going to have to get it cut. Maybe he was out cold for a lot longer than he had initially thought.

"Ah, I see. How far back is your earliest memory? Vat age, approximately?"

Peter closed his eyes and thought for a moment. A thousand memories sat in front of him, playing out short snippets. He dug backwards trying to recall his earliest memories. Eventually he had found one. It was him and his Uncle Ben tying his ice skates at Rockefeller Center he could see his bright blue mittens trying to grasp the strings to no avail. His uncle chuckled. "Don't worry sport, you'll get it one day."

"Three."

Ugh his voice sounded so weird. It was so high pitched, he sounded like a girl. He was almost sixteen. When would his voice finally deepen enough that things like this wouldn't make him sound like a girl?

The man spoke to himself again. "Note Subject Drew does still retain memories through the experiments process like Subject Caine, and Subject Riley. It is recommended that the similar process should be undergone for subject Drew's benefit."

Experiment? Peter really didn't like the sound of that. Before Peter could react, his spider sense went off. Something was going to happen to his left. He leaped to the right as an explosion shook the building. Peter went to push passed the man, only to realize that he had gone right through him. Maybe his eyes hadn't been playing tricks on him, as he saw a piece of the building's ceiling fall through the man. A hologram, really?

None the less, Peter burst through the doors into the hallway. Every step felt off, like he wasn't entirely used to his body after whatever sick experiment he had been put through. Pieces of debris burst out into the hallway followed by a man in a lab coat. Blood streamed from him as his body collided with the wall behind him. A hand print was burned into the man's chest leaving a pussy melted mess.

Peter rushed forward to aid the man who was attempting to crawl away from his chaser. The young hero was closing the distance between them when a figure emerged from the dusty air. He could make out a slim figure with chin length hair. They were about the same height, but the way this figure moved was terrifying. It was like watching the Winter Soldier stalk down its prey, ready for the kill.

Peter's heart punded in his chest. He held up his hands, clenching them in fists, ready to fight. He knew he still wasn't feeling himself, but he had to protect the man. He had to power to do something, even if it was only enough time for the man to run away. He could hear running from behind the figure. Peter wondered if it was help. It it was, who was it for, him, or the man bent on destroying anything and everything in this place.

When the figure had stepped out of the dust, Peter's heart almost stopped. He had to be imagining things because this man looked just like him.


	2. Chapter 2

No way in hell was this real? How could that guy look like him? Was this all a dream? Did they swap bodies or something? What the hell was going on? Peter was stunned. He couldn't move, he couldn't think. This was all too much for someone who had woken up only minutes ago.

The footsteps were closer and another small figure could be seen running through the dissipating smoke. As if Peter wasn't stunned enough when he saw the Winter Soldier wanna be, seeing yet another copy of his face really took the cake. This one however had shorter hair and was donned in a red costume with a light blue sleeveless hoodie with a black spider painted on. It was like he was falling further and further down the rabbit hole.

"Looks like we found the-" the red one started to say before leaning to look behind Peter. A look of pure distress was painted on his face. "Kaine! What the heck man? Look at that guy's chest!"

The one with longer hair spun on a dime, facing the duplicate in red, a fire burning bright in his eyes. "He was going to shoot us Ben, and its not like it's going to the kill the guy." The long haired copy looked at the scientist crawling away with a look of pure hatred, "Besides, Dr. Warren knew what I was capable of. He made us after all."

There was a particular tone of bitterness and spite in his voice that nearly made Peter shiver. He could tell that there was bad blood and this event was a long time in the making in just a few words. What the hell was this place? What did that guy mean? Did the scientist give those two powers, but then why did they look like him?

The two of the duplicates held a heated gaze for a moment before the one in red turned towards Peter. "I'm Ben by the way, and uh well we-"

He was cut off by the long haired one "Yeah, I think she caught it when I said it earlier dumb ass."

Peter looked around for a girl? Was there someone else here? He hadn't noticed anyone else show up? Who was that guy referring to?

Ben's eyes grew wide and he looked as though he had just revealed that there was going to be a surprise party for him on accident. The one with long hair pinched the bridge of his nose and shook his head. Had the one with short hair said something wrong, or just something stupid. Peter began to wonder when this would all begin to make sense.

"Frick, how long ago did you wake up?" Ben asked.

Peter's voice was caught in his throat? How did he know that? What was going on? Before he could even begin to fathom the situation, his thoughts were interrupted.

"Already forgetting the fricken plan already, aren't we Ben?" The long haired one spat out. "Grab Dr. Warren's phone. The three of us need to get out of here. Now!"

This wasn't real. None of this made sense. There was no way that he was going anywhere without an explanation. Besides, how could he trust the guy who burned a hole in that scientist's chest? There was no way he could trust this guy, but then again, how could he trust these scientists. There was some bad blood between his duplicates and the scientist after all. What had happened to them here to cause this?

Ben rushed over, snatching phone from the man's lab coat. "No signal in here. We'll have to get outside."

The one with long hair motioned for him to follow. "Come on! We'll explain on the way."

Peter took a few steps after them before coming to a halt. He saw the poor scientist, guilty or not, still struggling to escape the wreckage caused by the escapees.

"What about that guy?" Peter asked.

How could they just leave that man laying there? Sure he was probably a bad guy, but that didn't mean that they could just leave him there. Even Tooms deserved saving. I guess this would really test their character enough for them to prove themselves to him.

"Right, thanks." The one with long hair said.

In one quick action, the scientist was webbed to the wall behind him. His mouth was covered, but he was trying to yell something.

Ben let out a sigh and shrugged."I guess that will hold him until Mr. Stark shows up."

"Yeah, assuming was can get him here. Now come on!"

Reluctantly, Peter took off with the duplicates. They hadn't hurt the scientist even more, just restrained him. And they wanted to get Mr. Stark. How bad could they be if they were seeking him out. It was a comforting thought, seeing Mr. Stark so soon after everything had gone to hell in a hand basket.

As he started running, he noticed something was off. There were a couple of somethings there that weren't there before and a couple of things that were there, that now weren't. Had he swapped bodies with a girl? It would explain a lot. Peter wondered what Mr. Stark would say about this whole mess, a snarky comment no doubt. But it was something that was worth looking forward too.

"Kaine, Mr. Stark will come."

"What the frick frack is going on?" Peter asked, his feminine voice now ringing clear.

They were running down a maze of hallways. Sirens and red flashing lights were giving Peter a head ache as they ran. It was so weird running in this body. It felt unnatural, and he wasn't sure if it was because he was in a female body or not, but that was his best guess.

"We are currently escaping a HYDRA facility right second we are going to run into a bunch of bad guys who are going to try to stop us." Kaine said.

"They aren't going to kill us or anything." Ben added hastily.

Kaine rolled his eyes. "Yeah, the three of us are too valuable for that. There's no way they are going to want to start the cloning process all over. Not when they can knock us out and wipe away Peter's memories. They'll have their spider army they've been dreaming for and we can't let that happen."

"What?" Peter asked.

Clones? Well it made sense as to why there was two of them. But how did that explain the memories he had? How long had this been going on for? If he was in the body of a teenager, assuming those guys were about his age, how many years had passed since that armored car fight?

"The three of us, clones of Peter Parker. As to why you're a chick, who knows. Maybe a messed up Y gene, or a messed up idea, especially since we all have his memories still. But we had to get out of here before they wiped them away. I am not going to be used as an assassin for HYDRA and neither are you."

Ben nodded in agreement. At this point it was definitely clear that Kaine was the leader of the two. Peter wasn't sure if it was because of his "cheerful" demeanor, or if he was the oldest, just guessing on his longer hair. Either way, the anger beneath his surface was less that comforting. Then again being a creation of HYDRA wasn't comforting either. They had really messed with Bucky and there was no telling how they had already warped their three minds. Who knew how far this guy would go to escape, but with these kinds of stakes, maybe he, no they, needed to go that far. Upon rounding a corner to find a bunch of men donned in SWAT like armor adorned with HYDRA's symbol, he- no she, was about to get a good idea of that.


End file.
